Data for: Induction of C4 genes during de-etiolation of Gynandropsis gynandra evolved through changes in cis allowing integration into ancestral C3 gene regulatory networks

C4 photosynthesis has evolved repeatedly and in doing so repurposed existing enzymes to drive a carbon pump that limits the oxygenation reaction of RuBisCO. C4 proteins accumulate to levels matching those of the photosynthetic apparatus, and to allow this gene expression must be modified over evolutionary time. To better understand this rewiring of gene expression we undertook RNA-SEQ and DNaseI-SEQ on de-etiolating seedlings of C4 Gynandropsis gynandra which is evolutionarily proximate to C3 A. thaliana. Changes in chloroplast ultrastructure and C4 gene expression in G. gynandra were coordinated and rapid. C3 and C4 photosynthesis genes showed similar induction patterns, but C4 genes from G. gynandra were more strongly induced than orthologs from A. thaliana. The cistrome of G. gynandra was enriched in TGA, TCP and homeodomain binding sites. Furthermore, in vivo binding data in G. gynandra highlighted TGA and homeodomain as well as light responsive elements such as G- and I-box motifs as being associated with the rapid increase in transcripts derived from C4 genes. Although promoters of PPDK and ASP1 from G. gynandra contained distinct light responsive elements, promoters from both A. thaliana and G. gynandra allowed high expression. Deletion analysis of the Ppa6 gene from G. gynandra showed that regions containing G- and I-boxes were necessary for high expression. The data support a model in which accumulation of transcripts derived from C4 genes in leaves of G. gynandra is enhanced compared with homologs in A. thaliana because a variety of modifications in cis allowed integration into ancestral transcriptional networks.